Sunday, May 3, 2015

Ancestral character state reconstruction in Mesquite 3: parsimony versus likelihood

One of the more curious recent developments in my area is that some journals now make all reviewer reports available to all of the peer reviewers of a given manuscript. I like it because it allows me to get a better feeling for whether I have been too lenient or too critical, see other colleagues' style of making comments, and so on.

Very recently I have reviewed a manuscript, and just two days ago I saw what the second reviewer thought. Our recommendations turned out to be generally the same, but one sentence of theirs really annoyed me. When discussing ancestral character state reconstruction, they complained that all reconstructions in the present study were done "only" with parsimony.

Thursday, April 30, 2015

CBA Conference 2015, last day

The final day of the 2015 CBA conference on species delimitation featured another set of very interesting talks.

Sally Potter presented her and colleagues' exome capture pipeline for the study of skinks. Admittedly this was already so specific and applied that one would not expect to walk away with many concrete ideas for one's own work unless one wants to use pretty much the same method, but she also mentioned a species tree method that had so far escaped my attention.

ASTRAL is supposedly very fast for large numbers of loci; it is said to be "improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods". Statistical consistency sounds nice, but when I played around with them for a bit back when those precursor methods didn't really convince me. Still, ASTRAL may be worth a try at some point in the future.

Wednesday, April 29, 2015

CBA Conference, day 2

Continuing with the 2015 CBA conference on species delimitation.

Today's first speaker was Sasha Mikheyev, who presented genome sequencing data on hybridisation zones in social insects. Most of his talk focused on Africanised bees in America, where he was lucky enough to find collaborators who had a time series of samples in the freezer capturing exactly the moment when the African genes swamped populations in the southern United States. Important research, but the results were still preliminary, so he could not go into what he ultimately wants to find out about the dynamics of hybridisation.

He ended his talk with a really weird story about an ant species in which queens are clones of their mothers, males are clones of their fathers (how does that work - is there a zygote but the female chromosomes are discarded?), and only the workers are half-half. This means that the males and females of the same "species" are genetically completely isolated, and indeed the male lineage is more closely related to a different species than to the females they have sex with.

You just can't make anything up that is more bizarre than what reality holds in stock for us.

Tuesday, April 28, 2015

CBA Conference 2015, day 1

Most of this week I am at the 2015 CBA conference Species delimitation in the age of genomics.

Although the title suggests that you'd die of alcohol poisoning in short order if you took a drink every time you heard somebody claim that genomic data are going to solve all our problems, the actual talks happily do not fit that stereotype. Maybe people have seen enough genomic data now to dispense with the hyperbole.

Today started off with a talk by the Australian philosopher of science John Wilkins. He argued that the traditional approach taken by most people who are explicitly grappling with the species problem is to declare a theory-based species concept, try to force it onto reality, and then consider the species-ness to be an explanation for what we see in nature: This individual is the way it is because it is a member of that species. In Wilkins' opinion, that is precisely the wrong way around.

Sunday, April 26, 2015

Botany picture #200: Xeranthemum inapertum

Xeranthemum inapertum (Asteraceae), France, 2014. Here in Australia we have lots of Asteraceae in the paper daisy tribe Gnaphalieae that have lost the otherwise fairly daisy-typical petal-like ray florets but then went through the evolutionary equivalent of regretting that loss, so they evolved papery colourful radiating bracts to serve as pseudo-petals. In the Mediterranean area we can find two other groups of Asteraceae that have done precisely the same thing, only they belong to the thistle tribe Cardueae instead.

The above genus Xeranthemum consequently looks very unlike a thistle (and it doesn't even have spines). In fact the well-known golden everlasting Xerochrysum bracteatum, a typical Australian Gnaphalieae, was originally described as a Xeranthemum, the systematic equivalent of describing an Acacia as part of the clover genus Trifolium. Of course that was in 1803, and the mistake was corrected only two years later.

Thursday, April 23, 2015

Giving taxonomists recognition through citations

Today we discussed the recent Zootaxa paper Fried spicy Linnaeus (Kottelat, 2015) in our journal club. It is open access and a fun read, well worth checking out.

Kottelat discusses the pros and cons and potential variants of mentioning the taxonomic authority after Latin names of plants and animals. Well, mostly animals, but the same applies in all of biology. In botany, the usual format is as follows. Anemocarpa podolepidium (F.Muell.) Paul G.Wilson means that the species was originally described by the 19th century botanist Ferdinand Mueller in a different genus, as Helichrysum podolepidium F.Muell., and then later transferred into the genus Anemocarpa by Paul Wilson.

Botanical journals usually demand the author of a paper to give this full taxonomic authority the first time any species is mentioned but to leave it out afterwards, which can lead to rather odd looking sentences in which some species have the authority and others don't. In general, Kottelat argues convincingly, these authorities make the text clunky and do not usually add any information relevant to the reader.

On the other hand, many taxonomists are concerned that taxonomists should be given more, not less, recognition for the work they do. In botany at least the authorities as part of plant names do not count as bibliographic references and thus do not increase a taxonomist's number of citations. Because we are unfortunately evaluated based on how often people cite our work (as opposed to, say, how often they use it without citing it), many colleagues would like to see them turned into proper bibliographic references and would certainly not like them to disappear altogether.

Kottelat ultimately comes down in favour of turning them into full bibliographic references in taxonomic research papers and doing away with them in all other publications, a compromise that does not entirely convince me.

However, I really want to make a different point. I believe that the taxonomists who push for a rule requiring a bibliographic reference every time a species name is used vastly overestimate the utility of such a change.

Tuesday, April 21, 2015

Subsidence of the Pacific

A few days ago I expressed skepticicm about Michael Heads' claim, advanced in defence of the idea that the plants and animals of Hawaii did not get there through recent long distance dispersal but instead evolved in place for tens of millions of years, of the Pacific having undergone thousands of metres of subsidence over that time. Intuitively I was confident that that would have been impossible because most of the continents would have had to be under water.

I now stand corrected. I made a back of the envelope calculation using admittedly very conservative parameters, and it turns out that there is more continent than I thought:

The Pacific Ocean is 165.25 million km2 = 1.6525 x 10^14 m2 large. Assuming that a quarter of that area needed to have a 2,000 metres higher sea floor, the water displacement would be 2,000 m x 1.6525 x 10^14 m2 = 8.2625 x 10^16 m3. Assuming further that this needs to be distributed evenly across the surface of the planet, we would have the sea level higher by 8.2625 x 10^16 m3 / 5.1 x 10^14 m2 = 162 m.

Punching that number into, we see that by far most of the land is still above the sea:

Remember, of course, that I am leaning over backwards here. I have no idea if 25% of the Pacific and 2,000 metres would be enough or if Heads' claim involves larger numbers; that might change something (if you assume all of the Pacific, or half the Pacific and 4,000 metres, there is very little land left). Further, the Pacific was larger 65 million years ago than it is now, with the continents having drifted further apart. Of course the water would not be equally distributed either because the land displaces it too, so it would raise the oceans by more, but because most of the world is ocean that wouldn't matter so much. Perhaps more importantly though, if the floor is higher under the Pacific it has to be lower elsewhere, as there is a limited amount of Earth, and that would likely mean lower land masses at least somewhere.

For various other reasons I remain unconvinced of the vicariance scenario for Hawaii, but the subsidence of the Pacific is not as implausible as I naively assumed at the beginning, at least when using the above conservative estimates.